The original system proposed by Perpetual took this into account. (It was usually a design flaw which was posited on by everyone the second they heard about a Star Trek MMOG, immediately proceeding excitement at living and playing with a real crew.) When a player left a post, an NPC would (Fittingly much like the real series'.) leave a post, an NPC would take over, the NPC was both less effective than a player and also less fun than playing with a friend. It also allowed you to play the game solo if you should wish.
Of course this idea, fun, obvious, the first to come to mind of anyone thinking about a Star Trek MMOG, was eventually even slightly backed-off by Perpetual themselves and is certainly not on the agenda of Cryptic, who seem bent on getting STO out as quickly as they can.
We can expect a game more akin to the current generation of MMOGs which, despite their efforts to date having gained absolutely none of the market share WoW supposedly brought to the genre as a whole. Without the ability to walk around your ship (There is contradictory information on this, so at this point I will assume, based on screenshots that we can at least walk around the bridge) and live on it, as Perpetual originally envisioned, to have friends onboard with you, I can see something deeply missing. It also ruins the idea of the size of the starships, I have a fear they will interact and feel like the frigates in EvE.
Having said all of that, there are always the Klingons, I have no feelings of great fascination with their ships interiors because we rarely saw them and it was always dark and uninteresting and who cares if their ships handle like frigates, the Bird of Prey is supposed to do so! I will miss player crews, but they have been dead for years.